Interactive Volume Rendering of Functional Representations in Quantum Chemistry

Simulation and computation in chemistry studies have been improved as computational power has increased over decades. Many types of chemistry simulation results are available, from atomic level bonding to volumetric representations of electron density. However, tools for the visualization of the results from quantum chemistry computations are still limited to showing atomic bonds and isosurfaces or isocontours corresponding to certain isovalues. In this work, we study the volumetric representations of the results from quantum chemistry computations, and evaluate and visualize the representations directly on the GPU without resampling the result in grid structures. Our visualization tool handles the direct evaluation of the approximated wavefunctions described as a combination of Gaussian-like primitive basis functions. For visualizations, we use a slice based volume rendering technique with a 2D transfer function, volume clipping, and illustrative rendering in order to reveal and enhance the quantum chemistry structure. Since there is no need of resampling the volume from the functional representations, two issues, data transfer and resampling resolution, can be ignored, therefore, it is possible to interactively explore large amount of different information in the computation results.

[1]  Olga Kennard,et al.  Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds , 1987 .

[2]  Ivan Viola,et al.  Two-Level Approach to Efficient Visualization of Protein Dynamics , 2007, IEEE Transactions on Visualization and Computer Graphics.

[3]  Thomas Ertl,et al.  Visual Verification and Analysis of Cluster Detection for Molecular Dynamics , 2007, IEEE Transactions on Visualization and Computer Graphics.

[4]  Chandrajit L. Bajaj,et al.  TexMol: interactive visual exploration of large flexible multi-component molecular complexes , 2004, IEEE Visualization 2004.

[5]  Amitabh Varshney,et al.  Representing thermal vibrations and uncertainty in molecular surfaces , 2002, IS&T/SPIE Electronic Imaging.

[6]  Tao Zhang,et al.  Direct Volume Rendering of Volumetric Protein Data , 2006, Computer Graphics International.

[7]  Markus Hadwiger,et al.  Real‐Time Ray‐Casting and Advanced Shading of Discrete Isosurfaces , 2005, Comput. Graph. Forum.

[8]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation. , 2008, Journal of chemical theory and computation.

[9]  Michael Gleicher,et al.  Molecular Surface Abstraction , 2007, IEEE Transactions on Visualization and Computer Graphics.

[10]  David S. Ebert,et al.  Interactively visualizing procedurally encoded scalar fields , 2004, VISSYM'04.

[11]  David S. Ebert,et al.  Hub-based Simulation and Graphics Hardware Accelerated Visualization for Nanotechnology Applications , 2006, IEEE Transactions on Visualization and Computer Graphics.

[12]  Jane Wilhelms,et al.  DIRECT VOLUME RENDERING VIA 3D TEXTURES , 1994 .

[13]  Ho-Lun Cheng,et al.  Guaranteed quality triangulation of molecular skin surfaces , 2004, IEEE Visualization 2004.

[14]  James F. Blinn,et al.  Real-time GPU rendering of piecewise algebraic surfaces , 2006, SIGGRAPH 2006.

[15]  Klaus Schulten,et al.  High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs , 2009, GPGPU-2.

[16]  Rüdiger Westermann,et al.  Acceleration techniques for GPU-based volume rendering , 2003, IEEE Visualization, 2003. VIS 2003..

[17]  Andreas Kolb,et al.  A Vertex Program for Efficient Box-Plane Intersection , 2005 .

[18]  Thomas Ertl,et al.  Smart Hardware-Accelerated Volume Rendering , 2003, VisSym.

[19]  TariniMarco,et al.  Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization , 2006 .

[20]  David S. Ebert,et al.  VolQD: direct volume rendering of multi-million atom quantum dot simulations , 2005, VIS 05. IEEE Visualization, 2005..

[21]  Srinivasan Parthasarathy,et al.  Detection and visualization of anomalous structures in molecular dynamics simulation data , 2004, IEEE Visualization 2004.

[22]  David S. Ebert,et al.  Enhancing the Interactive Visualization of Procedurally Encoded Multifield Data with Ellipsoidal Basis Functions , 2006, Comput. Graph. Forum.

[23]  David S. Ebert,et al.  Illustration and photography inspired visualization of flows and volumes , 2005, VIS 05. IEEE Visualization, 2005..

[24]  Ketan Mehta,et al.  Detection and Visualization of Defects in 3D Unstructured Models of Nematic Liquid Crystals , 2006, IEEE Transactions on Visualization and Computer Graphics.

[25]  G. Schaftenaar,et al.  Molden: a pre- and post-processing program for molecular and electronic structures* , 2000, J. Comput. Aided Mol. Des..

[26]  Daniel Baum,et al.  Visualizing dynamic molecular conformations , 2002, IEEE Visualization, 2002. VIS 2002..

[27]  J. R.,et al.  Chemistry , 1929, Nature.

[28]  Ying Liu,et al.  Interactive molecule construction with GPU acceleration , 2008 .

[29]  David S. Ebert,et al.  Volume illustration: non-photorealistic rendering of volume models , 2000, Proceedings Visualization 2000. VIS 2000 (Cat. No.00CH37145).

[30]  Charles T. Loop,et al.  Real-time GPU rendering of piecewise algebraic surfaces , 2006, ACM Trans. Graph..